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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatgaatgagtactatgatgtttgcaattcgctgtctgctagtcatctagtttcttcttctatgatttgctagatatctagctatgcatgtggtctgcttgcag

Basic information

species Zea mays
transcript GRMZM2G096343_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 10
GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatgaatgagtactatgatgtttgcaattcgctgtctgctagtcatctagtttcttcttctatgatttgctagatatctagctatgcatgtggtctgcttgcag
|| || || |  || ||  ||||| ||||||||||||||||||| |||||||||||||||||||||| ||| ||||| |||||||||||||||||| |||   |||| |||| | ||  | |  ||                       |||| |||||   | |||| | ||  |||  |   |  | | |||||| | ||
GTCGGATCTGTTCTTCTCAGTTGTTCCTTCTTATATGACATCTTTTGGGTTTTTATCTCCAAGATGTGGTTTCATGAGAGTGTGATGATTGTGgtaggtacagatgactactttcatact-gtgatg----------------------ttctgcttctgcaacttgcgaaatg-ctaattgccctagcg-tctgctcgtag

upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA07G07610.1 (Glycine max), 5'ss of exon 11
GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatgaatgagtactatgatgtttgcaattcgctgtctgctagtcatctagtttcttcttctatgatttgctagatatctagctatgcatgtggtctgcttgcag
|| ||  | |  || ||  ||||||||||| ||||||||||||||||||| ||| |||| ||   || ||||||||| ||||||||||| |||||  || |     || || ||      |      |  | |   | |  | |  | |||   ||  ||     ||||   |  ||    |      |  ||| | | |||
GTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATATGACATCTTCTGGGTGTTTGTCTCTAAACGGTGGTTCCATGAGAGTGTGATGATAGTGgtgagtgttttaaagaacaatcccccgtctctaccattcttcacaaagc-ttgattttggcctcatacatgatgctgttttcctgttaaaattattattctccatacag

upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA03G01100.2 (Glycine max), 5'ss of exon 10
GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgta--tgtatgaatgagtactatgatgtttgcaattcgctgtctgctagtcatctagtttcttcttctatgatttgctagatatctagctatgcatgtggtctgcttgcag
|| ||  | |  || ||  ||||||||||| |||||||||| || ||||| ||| |||| ||   || ||||||||| ||||||||||| |||||   ||| | || ||    | |     |  || |   |     | |  |  | | |  || |     ||| | |                                    
GTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATATGACATTTTTTGGGTGTTTGTCTCTAAACGGTGgttccatgagagtgtgatgatagtggtgagtgttttaaagaaagttctccctctaccattcttcccaaagttgat--tttggcctcatacatgatgctgttt----------------------------------

upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA18G46760.1 (Glycine max), 5'ss of exon 10
GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatgaatgagtactatgatgtttgcaattcgctgtct---gctagtcatctagtttcttcttctatgatttgctagatatctagcta-tgca----tgtggtctgcttgcag
|| ||  | |  || ||  ||||||||||| |||| |||||||||||||| ||| |||| ||   || ||||||||| ||||||||||| |||||  ||      ||| |  ||     ||  | |   ||       ||| ||  | || | || |     |||||    |   |||  | ||| ||||    | |    |  ||||||
GTCGGAACTGTTCTTCTCAGTTGTGCCTTCCTATACGACATCTTCTGGGTGTTTGTCTCTAAATGGTGGTTCCATGAGAGTGTGATGATAGTGgtgagtgatttcgaggaagatctcccttagactattcttcacaaagcttgtttttta-tctcataaaacatgatgcttttcttattaaactaatgcaacattttcacttctttgcag

upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA11G02540.1 (Glycine max), 5'ss of exon 10
GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatgaatgagtactatgatgtttgcaattcgctgtctgctagtcatctagtttcttcttctatgatttgctagatatctagctatgcatgtggtctgcttgcag
|| ||| |||  || || || ||||||||| | || |||||||| ||||| ||| |||| |||| ||| ||| | |||||||| |||||||||||  |||| |     || | | ||   ||  | || || ||  |     || || || ||  || ||  ||||     |  | |  ||   |||               
GTTGGTACAGTACTTCTCGGCTGTGCCTTCATTTACGACATCTTTTGGGTGTTTGTCTCAAAGAAGTTTTTCAAGGAAAGTGTCATGATTGTGgttagtattatgctctattctaattcatgacaatcactatcaccc---tatgtatttactaatttta--atttttcttactttttactcaccatag-------------

upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA09G39500.1 (Glycine max), 5'ss of exon 10
GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgta--tgaatgagtactatgatgtttgcaat-tcgct--gtctgctagtcatctagt--ttcttcttctatgatttgctagatat-ctagctatgcatgtggtctgctt-gcag
|| ||  | |  || ||  ||||||||||| |||| |||||||||||||| ||| |||| ||   || ||||||||| ||||||||||| |||||  ||   |   ||     | |    |   |||| || |   |  || |  | ||||  |  | | |  |  ||| ||| ||   ||  |||      ||| |   || ||| ||||
GTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATACGACATCTTCTGGGTGTTTGTCTCTAAATGGTGGTTCCATGAGAGTGTGATGATAGTGgtgagtgatttcttggaagatctcccttcgacaatatcacaaagcttgtttttgatctcataatacatgattgatgcttttcttattaaactaatgcaacattttcacttctttgcag

upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA03G01100.1 (Glycine max), 5'ss of exon 10
GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatgaatgagtactatgatgtttgcaattcgctgt-ctgctagtcatctagtttcttcttctatgatttgctagatatctagctatgcatgtggtctgcttgcag
|| ||  | |  || ||  ||||||||||| |||||||||| || ||||| ||| |||| ||   || ||||||||| ||||||||||| |||||      || ||  |   |  | |||  |  |   |  | || |      |  | |||   ||  ||     ||||   |  ||    |      |  ||| | | |||
GTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATATGACATTTTTTGGGTGTTTGTCTCTAAACGGTGGTTCCATGAGAGTGTGATGATAGTGgt------gagtgttttaaagaaagttctccctctaccattcttcccaaagttgattttggcctcatacatgatgctgttttcctgttaaaattattattctccatacag

upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT1G63690.2 (Arabidopsis thaliana), 5'ss of exon 10
GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgta-----tgaatgagtactatgatgtttgcaattcgctgtctgctagtcatctagtt----tcttcttctatgatttgctagatatctagc-tatgcatgtggtctgcttgcag----------------------
|| ||  |||  || ||  | ||||||||||| || || ||||||||||| ||| ||||||||| ||||||||| ||||| || |||||||| ||| |||       ||| ||   |      |||   ||      |||   | |  || |  |    ||| |||     || | |   |  |||    | | || |          |  |                      
GTCGGGACAGTTCTTCTCAGCTGTGCCTTCTTGTACGATATCTTCTGGGTGTTTGTCTCCAAGAAGTTGTTCCACGAAAGCGTAATGATTGTCGTAAgtaaccaaccaatcagccatccaccattttgcataaagattctaacaatgctcaaactcaaatctcctttagaaatcttcatcacgtctcatatgttcaagaaaatgcaacgttgcttctttcttctttgcaggtag

upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT1G63690.1 (Arabidopsis thaliana), 5'ss of exon 10
GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgta-----tgaatgagtactatgatgtttgcaattcgctgtctgctagtcatctagtt----tcttcttctatgatttgctagatatctagc-tatgcatgtggtctgcttgcag------------------
|| ||  |||  || ||  | ||||||||||| || || ||||||||||| ||| ||||||||| ||||||||| ||||| || |||||||| ||| |||       ||| ||   |      |||   ||      |||   | |  || |  |    ||| |||     || | |   |  |||    | | || |          |  |                  
GTCGGGACAGTTCTTCTCAGCTGTGCCTTCTTGTACGATATCTTCTGGGTGTTTGTCTCCAAGAAGTTGTTCCACGAAAGCGTAATGATTGTCgtaagtaaccaaccaatcagccatccaccattttgcataaagattctaacaatgctcaaactcaaatctcctttagaaatcttcatcacgtctcatatgttcaagaaaatgcaacgttgcttctttcttctttgcag

upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT1G01650.1 (Arabidopsis thaliana), 5'ss of exon 10
GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatgaatgagt--------actatgatgtttgcaattcgctgtctgctagtc-atcta---gtttcttcttctatgatttgc-tagatatctagctatgcatgtg-gtctgcttgcag--------------
|| || |  |  || ||  | ||||||||| | ||||||||||||||||||||| | || ||   || ||||| |||||| ||||||||||||||| || |   |   |        || || |||   | ||  |  |||  | || || | |||    |   |   | | || |   |   |||||      |    |||  ||||  |  ||               
GTCGGGTTTGTTCTTCTCAGCTGTGCCTTCATGTATGACATCTTCTGGGTTTTTGTTTCAAAATGGTGGTTCCGTGAAAGCGTGATGATTGTGgtaagtttttcttttttgctccagaccatcatgcaag-aagactttgttagatattccaactacacatacttatctgtctgctccacactgatattatcggagaattgtacgtcttttcccattttcccacatatag

upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv02s0025g03400.t01 (Vitis vinifera), 5'ss of exon 10
GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatgaatgagtactatgatgt-ttgcaattcgctgtctgctagtcatctagtttcttcttctatgatttgctagatatctagctatgcatgtggtctgcttgcag--
|||||| |||  || ||  |||||||||| || || |||||||| ||||| ||  | || || | | ||||||||||||||||||||||||||||| |||    |   | |    || |  |  |    | |   ||    |||  || | |       |   | |  ||| | | |    ||     ||  | |  ||  |   
GTGGGTACAGTTCTTCTTAGTTGTGCCTTTTTGTACGACATCTTTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTGgtaagtactgcttttttcacccatatgctagaccatggttattgtggttcaaataatgtgcagactttcaaat-actaaaaagcattataaattggtcatgtttttatatag

upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv15s0046g02460.t01 (Vitis vinifera), 5'ss of exon 10
GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgta---tgaatgagtactatgatgtttgcaattcgct---gtctgctagtcatctagtttcttcttctatgatttgctagatatctagctatgca--tgtggtctgcttgcag
|| ||  | |  || ||  ||||||| ||||| || |||||||| ||||||||| | || ||   || |||| |||| |||||||||||||||||| |||   |     |    | | |      |||| |  |     | |||  |  | | ||   |           |  | |  ||   |  |||| |  |||| | |   |  ||
GTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTTTTTGTTTCTAAATGGTGGTTCAATGAGAGTGTGATGATTGTGgtaagtagtttctccaaaacttgttagcccaccaatacatttgaaacggctgat-gtttggtacttgagatctctgctgcccaattacagaattatgtaattgtgttttctgtatag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|76282121|gb|DV021689.1|DV021689
EST:     AAGATGTTGTTCCATGAAAGTGTGATGATTGTG                         GTTGCACGTGGTGACAAGACTGATGAGGATGGTGTACCCATGCTGTTAAAG
genomic: AAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatga ... ctgcttgcagGTTGCACGTGGTGACAAGACTGATGAGGATGGTGTACCCATGCTGTTAAAG
EST: gi|60344430|gb|DN211403.1|DN211403
EST:     TCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG                         GTTGCACGTGGTGACAAGACTGATGAGGATGGTGTACCCATGCTGTTAAAG
genomic: TCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatga ... ctgcttgcagGTTGCACGTGGTGACAAGACTGATGAGGATGGTGTACCCATGCTGTTAAAG
EST: gi|67041082|gb|CO467337.1|CO467337
EST:     TCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG                         GTTGCACGTGGTGACAAGACTGATGAGGATGGTGTACCCATGCTGTTAAAG
genomic: TCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatga ... ctgcttgcagGTTGCACGTGGTGACAAGACTGATGAGGATGGTGTACCCATGCTGTTAAAG
EST: gi|71422113|gb|DR805618.1|DR805618
EST:     AAGATGTTGTTCCATGAAAGTGTGATGATTGTG                         GTTGCACGTGGTGACAAGACTGATGAGGATGGTGTACCCATGCTGTTAAAG
genomic: AAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatga ... ctgcttgcagGTTGCACGTGGTGACAAGACTGATGAGGATGGTGTACCCATGCTGTTAAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatga ... ctgcttgcagGTTGCACGTGGTGACAAGACTGATGAGGATGGTGTACCCATGCTGTTAAAGATTCCTCGGATGTTTGATCCATGGGGTGGATACAGCATCATAGGCTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatga ... ctgcttgcagGTTGCACGTGGTGACAAGACTGATGAGGATGGTGTACCCATGCTGTTAAAGATTCCTCGGATGTTTGATCCATGGGGTGGATACAGCATCATAGGCTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 167

GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatga ... ctgcttgcagGTTGCACGTGGTGACAAGACTGATGAGGATGGTGTACCCATGCTGTTAAAGATTCCTCGGATGTTTGATCCATGGGGTGGATACAGCATCATAGGCTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatga ... ctgcttgcagGTTGCACGTGGTGACAAGACTGATGAGGATGGTGTACCCATGCTGTTAAAGATTCCTCGGATGTTTGATCCATGGGGTGGATACAGCATCATAGGCTTTG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTGgtatgtatgaatgagtactatgatgtttgcaattcgctgtctgctagtcatctagtttcttcttctatgatttgctagatatctagctatgcatgtggtctgcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG